Jump to main content
Jump to site search

Themed collection Mechanistic, computational & physical organic chemistry in OBC

50 items
Review Article

The importance of N-heterocyclic carbene basicity in organocatalysis

This review highlights the importance of N-heterocyclic carbene (NHC) basicity for transformations in which NHCs are used as catalysts.

Graphical abstract: The importance of N-heterocyclic carbene basicity in organocatalysis
Communication

Superelectrophilic activation of 1-nitronaphthalene in the presence of aluminum chloride. Reactions with benzene and cyclohexane

Aluminum chloride was successfully used instead of liquid superacids to mediate selective reactions of 1-nitronaphthalene with benzene and cyclohexane.

Graphical abstract: Superelectrophilic activation of 1-nitronaphthalene in the presence of aluminum chloride. Reactions with benzene and cyclohexane
Communication

Mechanism of nitrones and allenoates cascade reactions for the synthesis of dihydro[1,2-a]indoles

Quantum mechanical calculations (DLPNO-CCSD(T) and M06-2X) are employed to gain insights into the mechanism and selectivity in the catalytic synthesis of dihydropyrido[1,2-a]indoles from the cascade reaction between nitrones and allenes.

Graphical abstract: Mechanism of nitrones and allenoates cascade reactions for the synthesis of dihydro[1,2-a]indoles
From the themed collection: New Talent
Communication

A Viedma ripening route to an enantiopure building block for Levetiracetam and Brivaracetam

A simple route to enantiomerically pure (S)-2-aminobutyramide – the chiral component of the anti-epileptic drugs Levetiracetam and Brivaracetam has been developed. This approach is based on the rational design and application of a Viedma ripening process. The practical potential of the process is demonstrated on a large scale.

Graphical abstract: A Viedma ripening route to an enantiopure building block for Levetiracetam and Brivaracetam
Communication

Experimental evidence for the formation of cationic intermediates during iodine(III)-mediated oxidative dearomatization of phenols

Hammett analysis reveals iodine(III)-mediated oxidative dearomatization reactions proceed through cationic intermediates and not direct nucleophilic attack on an activated phenol.

Graphical abstract: Experimental evidence for the formation of cationic intermediates during iodine(iii)-mediated oxidative dearomatization of phenols
Communication

On the dual reactivity of a Janus-type mesoionic dipole: experiments and theoretical validation

A mesoionic bicycle, easily synthesized from a proteinogenic amino acid, L-leucine, behaves as both thiazolium-olate and diazolium-olate dipoles, as unveiled by its dipolar cycloadditions.

Graphical abstract: On the dual reactivity of a Janus-type mesoionic dipole: experiments and theoretical validation
Communication

A “cross-stitched” peptide with improved helicity and proteolytic stability

Peptide “cross-stitching” maintains binding affinity and can enhance helical and proteolytic stability.

Graphical abstract: A “cross-stitched” peptide with improved helicity and proteolytic stability
Paper

Computational insight into the mechanism and origins of high selectivities in the acylation of polyamines with 5-benzoyl-5-phenyl-1,5-dihydro-4H-pyrazol-4-one

Density functional theory was used to study the mechanism as well as the rate- and site-selectivities of the acylation reaction.

Graphical abstract: Computational insight into the mechanism and origins of high selectivities in the acylation of polyamines with 5-benzoyl-5-phenyl-1,5-dihydro-4H-pyrazol-4-one
Accepted Manuscript - Paper

Reactive cyclic intermediates in the ProTide prodrugs activation: Trapping the elusive pentavalent phosphorane

Paper

Understanding the mechanism and stereoselectivity of NHC-catalyzed [3 + 2] cycloaddition of 3-bromoenals and isatin N-Boc ketimines

The detailed mechanism and stereoselectivity of NHC-catalyzed [3 + 2] annulation between 3-bromoenals and isatin N-Boc ketimines have been investigated using a DFT method.

Graphical abstract: Understanding the mechanism and stereoselectivity of NHC-catalyzed [3 + 2] cycloaddition of 3-bromoenals and isatin N-Boc ketimines
Paper

Experimental and theoretical investigations of regioselective functionalization of 3-hydroxy bisindoles with thiols

An instant and efficient p-TSA·H2O-catalyzed sulfenylation reaction of 3-hydroxy bisindole derivatives is reported.

Graphical abstract: Experimental and theoretical investigations of regioselective functionalization of 3-hydroxy bisindoles with thiols
Accepted Manuscript - Paper

Unveiling the Role of the Strain of Cyclohexyne in [3+2] Cycloaddition Reactions through the Molecular Electron Density Theory

Paper

Regioselectivity of aryl radical attack onto isocyanates and isothiocyanates

Regioselectivity of attack by the N-methyl-pyridinium-4-yl radical cation onto RN[double bond, length as m-dash]C[double bond, length as m-dash]X (X = O and S) depends on R and X.

Graphical abstract: Regioselectivity of aryl radical attack onto isocyanates and isothiocyanates
Paper

Nazarov cyclisations initiated by DDQ-oxidised pentadienyl ether: a mechanistic investigation from the DFT perspective

The rate determining step for such a Nazarov cyclization is direct hydride transfer from pentadienyl ether to the oxygen of DDQ.

Graphical abstract: Nazarov cyclisations initiated by DDQ-oxidised pentadienyl ether: a mechanistic investigation from the DFT perspective
Paper

Exploiting the vicinal disubstituent effect on the diastereoselective synthesis of γ and δ lactones

Trifluoroacetic acid catalysed lactonization of vicinal disubstituted γ-hydroxyesters was investigated in different solvents.

Graphical abstract: Exploiting the vicinal disubstituent effect on the diastereoselective synthesis of γ and δ lactones
Paper

Mannich-type addition of 1,3-dicarbonyl compounds to chiral tert-butanesulfinyltrifluoroacetaldimines. Mechanistic aspects and chiroptical studies

Divergent diastereoselectivities are observed under quite different reaction conditions. An in-depth investigation of the chiroptical properties of the products has been carried out.

Graphical abstract: Mannich-type addition of 1,3-dicarbonyl compounds to chiral tert-butanesulfinyltrifluoroacetaldimines. Mechanistic aspects and chiroptical studies
Paper

Studies of 4-arylthiazolylhydrazones derived from 1-indanones as Trypanosoma cruzi squalene epoxidase inhibitors by molecular simulations

We present for the first time a study at the molecular level of the T. cruzi SE and the structural requirements for its inhibition.

Graphical abstract: Studies of 4-arylthiazolylhydrazones derived from 1-indanones as Trypanosoma cruzi squalene epoxidase inhibitors by molecular simulations
Paper

Investigations into the DNA-binding mode of doxorubicinone

Spectroscopic and calorimetric study of DNA-binding by doxorubicin and doxorubicinone found different binding modes for the two molecules, despite their structural homology.

Graphical abstract: Investigations into the DNA-binding mode of doxorubicinone
Paper

Origins of the enantioselectivity of a palladium catalyst with BINOL–phosphoric acid ligands

The enantioselectivity of the studied C–H activation is related to the Brønsted acidity and isopropyl groups of the effective catalysts.

Graphical abstract: Origins of the enantioselectivity of a palladium catalyst with BINOL–phosphoric acid ligands
Paper

A hemithioindigo molecular motor for metal surface attachment

We report on the synthesis of a hemithioindigo molecular motor bearing thioether feet for metal surface attachment and a comprehensive study of its light induced unidirectional motion in solution.

Graphical abstract: A hemithioindigo molecular motor for metal surface attachment
From the themed collection: New Talent
Paper

Local versus global aromaticity in azuliporphyrin and benziporphyrin derivatives

Magnetically induced current density calculations have elucidated the question of global versus local aromaticity in carbaporphyrinoids and their metal complexes.

Graphical abstract: Local versus global aromaticity in azuliporphyrin and benziporphyrin derivatives
Paper

Hydroarylation of unsaturated carbon–carbon bonds in cross-conjugated enynones under the action of superacid CF3SO3H or acidic zeolite HUSY. Reaction mechanism and DFT study on cationic intermediate species

Reactions of enynones with arenes in TfOH-Py or with zeolite HUSY lead to products of hydroarylation of the acetylene bond.

Graphical abstract: Hydroarylation of unsaturated carbon–carbon bonds in cross-conjugated enynones under the action of superacid CF3SO3H or acidic zeolite HUSY. Reaction mechanism and DFT study on cationic intermediate species
Paper

Competition between two cysteines in covalent binding of biliverdin to phytochrome domains

In this work, we disclose a mechanism of competing chemical reactions of protein assembly for a bacterial phytochrome using modern methods of molecular modeling.

Graphical abstract: Competition between two cysteines in covalent binding of biliverdin to phytochrome domains
Paper

Phosphinatophenylporphyrins tailored for high photodynamic efficacy

Porphyrin phosphinates are attractive candidates for photodynamic applications since their cellular uptake can be easily tuned by the substituent on phosphorus atoms.

Graphical abstract: Phosphinatophenylporphyrins tailored for high photodynamic efficacy
Paper

Understanding the axial chirality control of quinidine-derived ammonium cation-directed O-alkylation: a computational study

DFT calculations reveal the origins of axial chirality control by cinchona alkaloid derivatives.

Graphical abstract: Understanding the axial chirality control of quinidine-derived ammonium cation-directed O-alkylation: a computational study
From the themed collection: New Talent
Open Access Paper

Purine-substituted imidazolium mesomeric betaines and their tautomeric N-heterocyclic carbenes. Formation of a cyclic borane adduct

A purin-6-yl substituted imidazolium betaine underwent trapping reactions of its tautomeric N-heterocyclic carbene with sulfur, selenium, and triethylborane.

Graphical abstract: Purine-substituted imidazolium mesomeric betaines and their tautomeric N-heterocyclic carbenes. Formation of a cyclic borane adduct
Paper

An experimental and computational study on isomerically pure, soluble azaphthalocyanines and their complexes and boron azasubphthalocyanines of a varying number of aza units

Step by step insertion of aza units into non-aggregating isomerically pure azasubphthalocyanines Nx-[Spc*BCl] and azaphthalocyanines Nx-[Pc*M]: a systematic experimental and computational study on HOMO and LUMO energies.

Graphical abstract: An experimental and computational study on isomerically pure, soluble azaphthalocyanines and their complexes and boron azasubphthalocyanines of a varying number of aza units
Paper

Classical molecular dynamics and metadynamics simulations decipher the mechanism of CBP30 selectively inhibiting CBP/p300 bromodomains

The selective inhibition mechanism of CBP30 towards CBP/p300 over BRD4-BD1/BD2 bromodomains was revealed by conventional molecular dynamics and metadynamics simulations.

Graphical abstract: Classical molecular dynamics and metadynamics simulations decipher the mechanism of CBP30 selectively inhibiting CBP/p300 bromodomains
Paper

Why do A·T and G·C self-sort? Hückel aromaticity as a driving force for electronic complementarity in base pairing

Computations reveal that the potential for aromaticity gain and loss in nucleobases play key roles in modulating base pairing strengths.

Graphical abstract: Why do A·T and G·C self-sort? Hückel aromaticity as a driving force for electronic complementarity in base pairing
Paper

Elucidation of the catalytic mechanism of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase using QM/MM calculations

This account describes the application of QM/MM calculations to understand the reaction mechanism of HPPK, an important pharmacological target on the folate pathway for the treatment of diseases including anti-microbial resistance, malaria and cancer.

Graphical abstract: Elucidation of the catalytic mechanism of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase using QM/MM calculations
Paper

Computational study of the mechanism of amide bond formation via CS2-releasing 1,3-acyl transfer

A systematic computational study on CS2-releasing 1,3-acyl transfer was performed for the first time and provided deeper mechanistic insights.

Graphical abstract: Computational study of the mechanism of amide bond formation via CS2-releasing 1,3-acyl transfer
Paper

Heteroaryl-linked norbornadiene dimers with redshifted absorptions

The longest-wavelength absorption maximum of norbornadiene dimers with potential for molecular solar thermal systems can be finely tuned by varying the electronic nature of a heteroaryl spacer.

Graphical abstract: Heteroaryl-linked norbornadiene dimers with redshifted absorptions
Paper

A theoretical study on NHC-catalysed enantioselective cycloaddition of ketenes and 3-aroylcoumarins: mechanism and enantioselectivity

A DFT study of the NHC-catalysed 1 reaction of ketenes 2 with 3-aroylcoumarins 3 yielding dihydrocoumarin-fused dihydropyranones 4 is presented.

Graphical abstract: A theoretical study on NHC-catalysed enantioselective cycloaddition of ketenes and 3-aroylcoumarins: mechanism and enantioselectivity
Paper

Theoretical insight into the mechanism, regioselectivity, and substituent group effect of Rh-catalyzed synthesis of 1,2-benzothiazines from NH-sulfoximines and diazo compounds

A theoretical study of Rh-catalyzed synthesis of 1,2-benzothiazines from NH-sulfoximines and diazo compounds.

Graphical abstract: Theoretical insight into the mechanism, regioselectivity, and substituent group effect of Rh-catalyzed synthesis of 1,2-benzothiazines from NH-sulfoximines and diazo compounds
Paper

A DFT/PCM-based methodology for predicting solvolytic reactivities of organic carbonates

Reactivities of bicarbonate and various organic carbonate leaving groups were determined by using a very good correlation between calculated (IEFPCM/M06-2X) and measured heterolytic barriers.

Graphical abstract: A DFT/PCM-based methodology for predicting solvolytic reactivities of organic carbonates
Paper

Scope of the 2(5H)-furanone helicity rule: a combined ECD, VCD, and DFT investigation

Combination of ECD, VCD and DFT calculations revealed a possible exception to the widely used helicity rule of the 2(5H)-furanone chromophore.

Graphical abstract: Scope of the 2(5H)-furanone helicity rule: a combined ECD, VCD, and DFT investigation
Paper

An ab initio and DFT study of trifluoromethylation using Umemoto's reagent

Theoretical calculations revealed that trifluoromethylation using Umemoto's reagent would occur through the ionic backside mechanism.

Graphical abstract: An ab initio and DFT study of trifluoromethylation using Umemoto's reagent
Paper

The role of proton shuttling mechanisms in solvent-free and catalyst-free acetalization reactions of imines

Catalyst-free and solvent-free reactions of the type NuH + E → Nu–EH are NuH-catalyzed processes in which Grotthuss-like proton shuttling pays a key role.

Graphical abstract: The role of proton shuttling mechanisms in solvent-free and catalyst-free acetalization reactions of imines
Paper

A transition state “trapped”? QM-cluster models of engineered threonyl-tRNA synthetase

QM-cluster models demonstrate how protein bioengineering alters the local energy landscape of p-biphenylalanine to stabilize a transition state analogue.

Graphical abstract: A transition state “trapped”? QM-cluster models of engineered threonyl-tRNA synthetase
Paper

The effect of varying the anion of an ionic liquid on the solvent effects on a nucleophilic aromatic substitution reaction

Variety of ionic liquids with different anions used as solvents for a nucleophilic aromatic substitution reaction.

Graphical abstract: The effect of varying the anion of an ionic liquid on the solvent effects on a nucleophilic aromatic substitution reaction
Paper

Mechanistic studies of 1,3-dipolar cycloadditions of bicyclic thioisomünchnones with alkenes. A computational rationale focused on donor–acceptor interactions

Unlike monocyclic mesoionic dipoles, bicyclic thioisomünchnones provide high levels of regio- and stereoselection leading to heteroatom-rich polycycles.

Graphical abstract: Mechanistic studies of 1,3-dipolar cycloadditions of bicyclic thioisomünchnones with alkenes. A computational rationale focused on donor–acceptor interactions
Paper

The control of stereochemistry by the pentafluorosulfanyl group

The steric and electron withdrawing effects of the pentafluorosulfanyl group effectively direct the diastereoselectivity of the Staudinger reaction.

Graphical abstract: The control of stereochemistry by the pentafluorosulfanyl group
Paper

Potassium fluoride activation for the nucleophilic fluorination reaction using 18-crown-6, [2.2.2]-cryptand, pentaethylene glycol and comparison with the new hydro-crown scaffold: a theoretical analysis

Ion-pair binding in the hydro-crown ether leads to more effective catalytic cycle for nucleophilic fluorination.

Graphical abstract: Potassium fluoride activation for the nucleophilic fluorination reaction using 18-crown-6, [2.2.2]-cryptand, pentaethylene glycol and comparison with the new hydro-crown scaffold: a theoretical analysis
Paper

Probing the mechanism of thermally driven thiol-Michael dynamic covalent chemistry

The thermally driven exchange of thiol-Michael adducts is investigated, elucidating the underlying mechanism of this dynamic covalent process.

Graphical abstract: Probing the mechanism of thermally driven thiol-Michael dynamic covalent chemistry
Paper

A QM/MM approach on the structural and stereoelectronic factors governing glycosylation by GTF-SI from Streptococcus mutans

This manuscript contains novel insights into the reaction mechanism catalyzed by GTF-SI. Structural and electronic features of the system are revealed, such as the strong hydrogen bond depicted above.

Graphical abstract: A QM/MM approach on the structural and stereoelectronic factors governing glycosylation by GTF-SI from Streptococcus mutans
Paper

Structural revision of two unusual rhamnofolane diterpenes, curcusones I and J, by means of DFT calculations of NMR shifts and coupling constants

The structures of two unusual rhamnofolane diterpenes, curcusones I and J, have been revised using quantum calculations of NMR shifts.

Graphical abstract: Structural revision of two unusual rhamnofolane diterpenes, curcusones I and J, by means of DFT calculations of NMR shifts and coupling constants
Open Access Paper

The role of catalytic residue pKa on the hydrolysis/transglycosylation partition in family 3 β-glucosidases

The catalytic acid/base residue (E441) pKa, as modulated by its electrostatic environment, has potential impact on the hydrolysis/transglycosylation partition in β-glucosidases.

Graphical abstract: The role of catalytic residue pKa on the hydrolysis/transglycosylation partition in family 3 β-glucosidases
Paper

“Snorkelling” vs. “diving” in mixed micelles probed by means of a molecular bathymeter

A molecular bathymeter based on a carboxylic acid linked to a signalling fluorophore proves “snorkelling” vs. “diving” in mixed micelles.

Graphical abstract: “Snorkelling” vs. “diving” in mixed micelles probed by means of a molecular bathymeter
Paper

A computational investigation of the solvent-dependent enantioselective intramolecular Morita–Baylis–Hillman reaction of enones

A DFT study of the enantioselective organocatalytic intramolecular Morita–Baylis–Hillman (IMBH) reaction of enones under the influence of 1,1,1,3,3,3-hexafluoroisopropanol is reported. This study establishes an excellent fit between the experiment and theory.

Graphical abstract: A computational investigation of the solvent-dependent enantioselective intramolecular Morita–Baylis–Hillman reaction of enones
Open Access Paper

Structure–reactivity correlations of the abnormal Beckmann reaction of dihydrolevoglucosenone oxime

Structural, spectroscopic and computational studies of a series of oximes reveals ground state structural manifestations relevant to the reaction coordinate for the Beckmann rearrangement (normal Beckmann) and Beckmann fragmentation (abnormal Beckmann).

Graphical abstract: Structure–reactivity correlations of the abnormal Beckmann reaction of dihydrolevoglucosenone oxime
50 items

About this collection

The latest articles published in Organic and Biomolecular Chemistry related to mechanistic, computational & physical organic chemistry research.

Spotlight

Advertisements